MolNFT v1 · #151842 · protein
Crystal structure of human dermatan sulfate epimerase 1
6HZN · Dermatan-sulfate epimerase: “Crystal structure of human dermatan sulfate epimerase 1”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.55). MolNFT v1 #151842 on GenesisL1: 3D structure, binding sites…
- PDB
- 6HZN
- Type
- protein
- Length
- 743 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dermatan-sulfate epimerase
- EC
- 5.1.3.19
- UniProt
- Q9UL01
- Ligands
- NAG, MAN, BMA, MN
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dermatan-sulfate epimerase (EC 5.1.3.19) | protein | 743 | 37% helix, 20% strand | Q9UL01 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MN · Manganese (II) ion · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.55 | 0.82 | 16 | empty |
| 2 | 140 | 0.54 | 0.81 | 23 | empty |
| 3 | 170 | 0.51 | 0.78 | 18 | empty |
| 4 | 200 | 0.48 | 0.75 | 30 | empty |
| 5 | 84 | 0.48 | 0.82 | 17 | empty |
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9UL01
- Elsewhere: RCSB PDB 6HZN · PDBe 6HZN · UniProt Q9UL01
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